Cable cell probing and sampling

../_images/probe_sample-diag.svg

A schematic view of how handles let you access sampled data measured at a probeset. A probeset is a probe placed on a locset (which may describe more than one point). When setting a probe on a locset a sampler is created. When this sampler is set to sampling (at a certain schedule), a handle is returned. This figure demonstrates how sampling data can be accessed through the handle associated to the probeset. See below for a possible result for data.

print(data) # The probe data printed, as found in single_cell_recipe.py
[[ 0.00000000e+00 -4.00000000e+01]
 [ 1.00000000e-01 -5.40211646e+01]
 [ 2.00000000e-01 -6.19670534e+01]
 ...
 [ 2.99000000e+01 -6.44564354e+01]]

Sample data recorded by the Arbor simulation object is returned in the form of a NumPy array, with the first column holding sample times, and subsequent columns holding the corresponding scalar- or vector-valued sample.

Probesets are defined over a location expression and will describe zero, one, or more probes, one per site. They are evaluated in the context of the cell on which the probe is attached.

Vector probes are a kind of probes that samples over a region, rather than a locset. This means that they may output more than a single data point per timestamp. The layout of the outputs as returned by samples() is slightly different, but contains the same sort of information as regular probesets.

../_images/probe_sample_vector-diag.svg

The structure of the data returned is slightly different when a vector probe is sampled. The same kind of information is included however. Instead of returning a list per probe in a probeset, the data and metadata now have an extra dimension to cover for the multitude of subregions.

Each of the functions described below generates an opaque probe object for use in the recipe recipe.probes() method.

More information on probes, probe metadata, and sampling can be found in the documentation for the class simulation.

Note

Cable cell probesets are defined analogously to their counterparts in the C++ API (see 5. Probes for details). Some details like probe_tag are not exposed in Python, as having Python probe callbacks has proven to be too slow.

Example

import arbor

tree = arbor.segment_tree()
p = tree.append(arbor.mnpos, arbor.mpoint(-3, 0, 0, 3), arbor.mpoint(3, 0, 0, 3), tag=1)
tree.append(p, arbor.mpoint(3, 0, 0, 3), arbor.mpoint(-3, 0, 0, 3), tag=2)
tree.append(p, arbor.mpoint(3, 0, 0, 3), arbor.mpoint(-3, 0, 0, 3), tag=2)

decor = (
   arbor.decor()
   .set_property(Vm=-40)
   .paint('"soma"', arbor.density("hh"))
   .place('"midpoint"', arbor.iclamp(10, 2, 0.8), "iclamp"))

cell = arbor.cable_cell(tree, labels, decor)

class single_recipe(arbor.recipe):
   def __init__(self):
      arbor.recipe.__init__(self)

   def num_cells(self):
      return 1

   def cell_kind(self, gid):
      return arbor.cell_kind.cable

   def cell_description(self, gid):
      return cell

   def probes(self, gid):
      return [arbor.cable_probe_membrane_voltage('(location 0 0.5)'),
               arbor.cable_probe_membrane_voltage_cell(),
               arbor.cable_probe_membrane_voltage('(join (location 0 0) (location 0 1))'),
               ]

   # (4.6) Override the global_properties method
   def global_properties(self, kind):
      return arbor.neuron_cable_properties()

recipe = single_recipe()
sim = arbor.simulation(recipe)
handles = [sim.sample((0, n), arbor.regular_schedule(0.1))
         for n in range(3) ]
sim.run(tfinal=1)

for hd in handles:
   print("Handle", hd)
   for d, m in sim.samples(hd):
      print(" * Meta:", m)
      print(" * Payload:", d.shape)

This script, has a single (scalar) probe, a single vector probe, and a probeset involving two scalar probes. The script is complete and can be run with Arbor installed, and will output:

Handle 0
* Meta: (location 0 0.5)
* Payload: (10, 2)
Handle 1
* Meta: [(cable 0 0 1), (cable 0 1 1), (cable 1 0 0), (cable 2 0 0), (cable 1 0 1), (cable 2 0 1)]
* Payload: (10, 7)
Handle 2
* Meta: (location 0 0)
* Payload: (10, 2)
* Meta: (location 0 1)
* Payload: (10, 2)

API

class arbor.probe

An opaque object that is the Python representation of probe_info.

See below for ways to create probes.

Membrane voltage
arbor.cable_probe_membrane_voltage(where)

Cell membrane potential (mV) at the sites specified by the location expression string where. This value is spatially interpolated.

Metadata: the explicit location of the sample site.

arbor.cable_probe_membrane_voltage_cell()

Cell membrane potential (mV) associated with each cable in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Axial current
arbor.cable_probe_axial_current(where)

Estimation of intracellular current (nA) in the distal direction at the sites specified by the location expression string where.

Metadata: the explicit location of the sample site.

Ionic current
arbor.cable_probe_ion_current_density(where, ion)

Transmembrane current density (A/m²) associated with the given ion at sites specified by the location expression string where.

Metadata: the explicit location of the sample site.

arbor.cable_probe_ion_current_cell(ion)

Transmembrane current (nA) associated with the given ion across each cable in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Total ionic current
arbor.cable_probe_total_ion_current_density(where)

Transmembrane current density (A/m²) _excluding_ capacitive currents at the sites specified by the location expression string where.

Metadata: the explicit location of the sample site.

arbor.cable_probe_total_ion_current_cell()

Transmembrane current (nA) _excluding_ capacitive currents across each cable in each CV of the cell discretization. Stimulus currents are not included.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Total transmembrane current
arbor.cable_probe_total_current_cell()

Transmembrane current (nA) including capacitive currents across each cable in each CV of the cell discretization. Stimulus currents are not included.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Total stimulus current
arbor.cable_probe_stimulus_current_cell()

Total stimulus current (nA) across each cable in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Density mechanism state variable
arbor.cable_probe_density_state(where, mechanism, state)

The value of the state variable state in the density mechanism mechanism at the sites specified by the location expression where.

Metadata: the explicit location of the sample site.

arbor.cable_probe_density_state_cell(mechanism, state)

The value of the state variable state in the density mechanism mechanism on each cable in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Point process state variable
arbor.cable_probe_point_state(target, mechanism, state)

The value of the state variable state in the point process mechanism associated with the target index target on the cell. If the given mechanism is not associated with the target index, no probe will be generated.

Metadata: an object of type cable_point_probe_info, comprising three fields:

  • target: target index on the cell;

  • multiplicity: number of targets sharing the same state in the discretization;

  • location: location object corresponding to the target site.

arbor.cable_probe_point_state_cell(mechanism, state)

The value of the state variable state in the point process mechanism at each of the targets where that mechanism is defined.

Metadata: a list of cable_point_probe_info values, one for each matching target.

Kind: vector probe.

Ionic internal concentration
arbor.cable_probe_ion_int_concentration(where, ion)

Ionic internal concentration (mmol/L) of the given ion at the sites specified by the location expression string where.

Metadata: the explicit location of the sample site.

arbor.cable_probe_ion_int_concentration_cell(ion)

Ionic internal concentration (mmol/L) of the given ion in each able in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.

Ionic external concentration
arbor.cable_probe_ion_ext_concentration(where, ion)

Ionic external concentration (mmol/L) of the given ion at the sites specified by the location expression string where.

Metadata: the explicit location of the sample site.

arbor.cable_probe_ion_ext_concentration_cell(ion)

Ionic external concentration (mmol/L) of the given ion in each able in each CV of the cell discretization.

Metadata: the list of corresponding cable objects.

Kind: vector probe.